def run_once(self, job_dir, ** kwargs):
from neuromllite.utils import print_v
from neuromllite.utils import load_simulation_json,load_network_json
from neuromllite.NetworkGenerator import generate_and_run
from pyneuroml.pynml import get_value_in_si
print_v('Running NeuroMLlite simulation in dir: %s...'%job_dir)
sim = load_simulation_json(self.nmllite_sim)
import random
sim.id = '%s%s'%(sim.id, '_%s'%kwargs['reference'] if 'reference' in kwargs else '')
network = load_network_json(self.base_dir+'/'+sim.network)
for a in kwargs:
if a in network.parameters:
print_v(' Setting %s to %s in network...'%(a, kwargs[a]))
network.parameters[a] = kwargs[a]
elif a in sim.fields:
print_v(' Setting %s to %s in simulator...'%(a, kwargs[a]))
setattr(sim,a,kwargs[a])
else:
print_v(' Cannot set parameter %s to %s in network or simulator...'%(a, kwargs[a]))
traces, events = generate_and_run(sim,
simulator = self.simulator,
network = network,
return_results = True,
base_dir = self.base_dir,
target_dir = job_dir)
print_v("Returned traces: %s, events: %s"%(traces.keys(), events.keys()))
return traces, events
def __init__(self,
runner,
vary,
fixed={},
verbose=False,
num_parallel_runs=1,
plot_all=False,
save_plot_all_to=None,
heatmap_all=False,
save_heatmap_to=None,
heatmap_lims=None,
show_plot_already=False,
peak_threshold=0):
self.sim = load_simulation_json(runner.nmllite_sim)
self.colormap = 'jet'
ps_id = 'ParamSweep_%s_%s' % (self.sim.id, time.ctime().replace(
' ', '_').replace(':', '.'))
print_v(
"Initialising ParameterSweep %s with %s, %s (%i parallel runs)" %
(ps_id, vary, fixed, num_parallel_runs))
os.mkdir(ps_id)
self.result_dir = os.path.abspath(ps_id)
self.runner = runner
self.fixed = fixed
self.vary = vary
self.verbose = verbose
self.num_parallel_runs = num_parallel_runs
self.plot_all = plot_all
self.save_plot_all_to = save_plot_all_to
self.heatmap_all = heatmap_all
self.save_heatmap_to = save_heatmap_to
self.heatmap_lims = heatmap_lims
self.show_plot_already = show_plot_already
self.index = 0
self.total_todo = 1
self.report = OrderedDict()
self.report['Varied parameters'] = vary
self.report['Fixed parameters'] = fixed
self.report['Simulations'] = OrderedDict()
for v in vary:
self.total_todo *= len(vary[v])
self.analysis_var = {
'peak_delta': 0,
'baseline': 0,
'dvdt_threshold': 0,
'peak_threshold': peak_threshold
}
if self.plot_all:
self.ax = pynml.generate_plot(
[],
[], # Add 2 sets of y values
"Traces generated from %s" % self.sim.id, # Title
labels=[],
xaxis='Time (ms)', # x axis legend
yaxis='Membrane potential (mV)', # y axis legend
title_above_plot=True,
show_plot_already=False) # Save figure
if self.heatmap_all:
if len(self.vary) != 1:
raise Exception(
'Heatmap can only be used when only one parameter is varied...'
)
self.hm_x = None
self.hm_y = []
self.hm_z = []
def __init__(self, nml_sim_file, parent=None):
"""Constructor for the GUI"""
super(NMLliteUI, self).__init__(parent)
self.SPIKES_RASTERPLOT = "Rasterplot"
self.SPIKES_POP_RATE_AVE = "Pop rate averages"
#print('Styles available: %s'%QStyleFactory.keys())
QApplication.setStyle(QStyleFactory.create('Fusion'))
header_font = QFont()
header_font.setBold(True)
self.backup_colors = {} # to ensure consistent random colors for traces...
self.simulation = load_simulation_json(nml_sim_file)
self.sim_base_dir = dirname(nml_sim_file)
if len(self.sim_base_dir) == 0:
self.sim_base_dir = '.'
self.network = load_network_json('%s/%s' % (self.sim_base_dir, self.simulation.network))
nameLabel = QLabel("NMLlite file: %s" % realpath(nml_sim_file))
nameLabel.setFont(header_font)
paramLayout = QGridLayout()
topLayout = QGridLayout()
midLayout = QGridLayout()
self.tabs = QTabWidget()
self.nmlliteTab = QWidget()
self.nml2Tab = QWidget()
self.matrixTab = QWidget()
self.tabs.resize(300, 200)
# Add tabs
self.simTab = QWidget()
self.tabs.addTab(self.simTab, "Simulation")
self.simTabLayout = QGridLayout()
self.simTab.setLayout(self.simTabLayout)
self.plotTabs = QTabWidget()
self.tracesTab = QWidget()
self.plotTabs.addTab(self.tracesTab, "Traces")
self.heatmapTab = QWidget()
self.plotTabs.addTab(self.heatmapTab, "Heatmap")
if self.simulation.plots2D is not None:
self.plot2DTab = QTabWidget()
self.plotTabs.addTab(self.plot2DTab, "2D plots")
self.plot2DTabLayout = QGridLayout()
self.plot2DTab.setLayout(self.plot2DTabLayout)
for plot2D in self.simulation.plots2D:
info = self.simulation.plots2D[plot2D]
pLayout = self.add_tab(plot2D, self.plot2DTab, figure=True, toolbar=True, options=True)
if self.simulation.plots3D is not None:
self.plot3DTab = QTabWidget()
self.plotTabs.addTab(self.plot3DTab, "3D plots")
self.plot3DTabLayout = QGridLayout()
self.plot3DTab.setLayout(self.plot3DTabLayout)
for plot3D in self.simulation.plots3D:
info = self.simulation.plots3D[plot3D]
pLayout = self.add_tab(plot3D, self.plot3DTab, figure=True, toolbar=False, options=True)
offset_opt = 1
rasterOptionsLayout = self.add_tab(self.SPIKES_RASTERPLOT,self.plotTabs, figure=True, toolbar=True, options=True)
self.rasterLegend = QCheckBox("Show legend")
self.rasterLegend.setChecked(True)
rasterOptionsLayout.addWidget(self.rasterLegend, 0, 0+offset_opt)
self.rasterLegend.toggled.connect(self.replotSimResults)
self.rasterInPops = QCheckBox("Include input pops")
self.rasterInPops.setChecked(True)
rasterOptionsLayout.addWidget(self.rasterInPops, 0, 1+offset_opt)
self.rasterInPops.toggled.connect(self.replotSimResults)
spikeStatOptionsLayout = self.add_tab(self.SPIKES_POP_RATE_AVE,self.plotTabs, figure=True, toolbar=True, options=True)
self.spikeStatInPops = QCheckBox("Include input pops")
self.spikeStatInPops.setChecked(True)
spikeStatOptionsLayout.addWidget(self.spikeStatInPops, 0, 0+offset_opt)
self.spikeStatInPops.toggled.connect(self.replotSimResults)
self.simTabLayout.addWidget(self.plotTabs)
self.tracesTabTopLayout = QGridLayout()
self.tracesTab.setLayout(self.tracesTabTopLayout)
self.tracesTabOptionsLayout = QGridLayout()
self.tracesTabTopLayout.addLayout(self.tracesTabOptionsLayout, 0, 0)
self.showTracesLegend = QCheckBox("Legend")
self.tracesTabOptionsLayout.addWidget(self.showTracesLegend, 0, 0)
self.traceSelectButton = QPushButton("Select traces...")
self.traceSelectButton.show()
self.traceSelectButton.setEnabled(False)
self.traceSelectButton.clicked.connect(self.traceSelect)
self.tracesTabOptionsLayout.addWidget(self.traceSelectButton, 0, 1)
self.tracesTabLayout = QGridLayout()
self.tracesTabTopLayout.addLayout(self.tracesTabLayout, 1, 0)
self.heatmapLayout = QGridLayout()
self.heatmapTab.setLayout(self.heatmapLayout)
self.heatmapColorbar = None
self.tracesFigure = Figure()
self.tracesCanvas = FigureCanvas(self.tracesFigure)
self.tracesToolbar = NavigationToolbar(self.tracesCanvas, self)
self.tracesTabLayout.addWidget(self.tracesCanvas)
self.tracesTabLayout.addWidget(self.tracesToolbar)
self.heatmapFigure = Figure()
self.heatmapCanvas = FigureCanvas(self.heatmapFigure)
self.heatmapLayout.addWidget(self.heatmapCanvas)
self.add_tab(self.GRAPH_TAB, self.tabs, image=True, options = True)
graphTabOptionsLayout = self.all_options_layouts[self.GRAPH_TAB]
offset_opt = 4
graphTabOptionsLayout.addWidget(QLabel("Graph level:"), 0, offset_opt+0)
self.graphLevelComboBox = QComboBox(self)
self.graphLevelComboBox.addItem('-3')
self.graphLevelComboBox.addItem('-2')
self.graphLevelComboBox.addItem('-1')
self.graphLevelComboBox.addItem('0')
self.graphLevelComboBox.addItem('1')
self.graphLevelComboBox.addItem('2')
self.graphLevelComboBox.addItem('3')
self.graphLevelComboBox.addItem('4')
self.graphLevelComboBox.addItem('5')
self.graphLevelComboBox.addItem('6')
self.graphLevelComboBox.setCurrentIndex(6)
graphTabOptionsLayout.addWidget(self.graphLevelComboBox, 0, offset_opt+1)
self.graphLevelComboBox.currentIndexChanged.connect(self.showGraph)
self.graphTypeComboBox = QComboBox(self)
self.graphTypeComboBox.addItem('d - dot')
self.graphTypeComboBox.addItem('c - circo')
self.graphTypeComboBox.addItem('n - neato')
self.graphTypeComboBox.addItem('f - fdp')
self.graphTypeComboBox.setCurrentIndex(0)
graphTabOptionsLayout.addWidget(QLabel("GraphViz engine:"), 0, offset_opt+2)
graphTabOptionsLayout.addWidget(self.graphTypeComboBox, 0, offset_opt+3)
self.graphTypeComboBox.currentIndexChanged.connect(self.showGraph)
self.graphShowExtInputs = QCheckBox("Show ext inputs")
self.graphShowExtInputs.setChecked(True)
graphTabOptionsLayout.addWidget(self.graphShowExtInputs, 0, offset_opt+4)
self.graphShowExtInputs.toggled.connect(self.showGraph)
self.graphShowInputPops = QCheckBox("Show input pops")
self.graphShowInputPops.setChecked(True)
graphTabOptionsLayout.addWidget(self.graphShowInputPops, 0, offset_opt+5)
self.graphShowInputPops.toggled.connect(self.showGraph)
self.add_tab(self.LEMS_VIEW_TAB, self.tabs, image=True, options = True)
self.add_tab(self.IMAGE_3D_TAB, self.tabs, image=True, options = True)
self.tabs.addTab(self.matrixTab, "Matrix")
self.matrixTabLayout = QGridLayout()
self.matrixTab.setLayout(self.matrixTabLayout)
# Add tabs
self.tabs.addTab(self.nmlliteTab, "NeuroMLlite")
self.nmlliteTabLayout = QGridLayout()
self.nmlliteTab.setLayout(self.nmlliteTabLayout)
self.nmlliteTabs = QTabWidget()
self.nmlliteTabLayout.addWidget(self.nmlliteTabs)
self.nmlliteSimTab = QWidget()
self.nmlliteTabs.addTab(self.nmlliteSimTab, "Simulation")
self.nmlliteSimTabLayout = QGridLayout()
self.nmlliteSimTab.setLayout(self.nmlliteSimTabLayout)
self.nmlliteSimText = QPlainTextEdit()
self.nmlliteSimTabLayout.addWidget(self.nmlliteSimText,0,0)
self.nmlliteNetTab = QWidget()
self.nmlliteTabs.addTab(self.nmlliteNetTab, "Network")
self.nmlliteNetTabLayout = QGridLayout()
self.nmlliteNetTab.setLayout(self.nmlliteNetTabLayout)
self.nmlliteNetText = QPlainTextEdit()
self.nmlliteNetTabLayout.addWidget(self.nmlliteNetText,0,0)
self.tabs.addTab(self.nml2Tab, "NeuroML 2")
self.nml2Layout = QGridLayout()
self.nml2Tab.setLayout(self.nml2Layout)
self.nml2Text = QPlainTextEdit()
self.nml2Text.insertPlainText("\n Generate an instance of the populations and projections in this network in NeuroML 2"+
"\n format by pressing the Generate NeuroML 2 button on the left"+
"\n\n\n WARNING: depending on the size of the generated network, text may take some time to load!")
self.nml2Layout.addWidget(self.nml2Text,0,0)
# Add tabs to widget
midLayout.addWidget(self.tabs, 0, 0)
mainLayout = QGridLayout()
topLayout.addWidget(nameLabel, 0, 0)
#topLayout.addWidget(self.nameLine, 0, 1)
rows = 0
l = QLabel("Network parameters")
l.setFont(header_font)
paramLayout.addWidget(l, rows, 0)
self.param_entries = {}
if self.network.parameters is not None and len(self.network.parameters) > 0:
for p in sorted(self.network.parameters.keys()):
rows += 1
pval = self.network.parameters[p]
label = QLabel("%s" % p)
paramLayout.addWidget(label, rows, 0)
entry = self.get_value_entry(p, pval, self.param_entries)
paramLayout.addWidget(entry, rows, 1)
if self.network.seed is not None:
rows += 1
pval = self.network.seed
label = QLabel('Net generation seed')
paramLayout.addWidget(label, rows, 0)
entry = self.get_value_entry('seed', pval, self.param_entries)
paramLayout.addWidget(entry, rows, 1)
if self.network.temperature is not None:
rows += 1
pval = self.network.temperature
label = QLabel('Temperature')
paramLayout.addWidget(label, rows, 0)
entry = self.get_value_entry('temperature', pval, self.param_entries)
paramLayout.addWidget(entry, rows, 1)
self.graphButton = QPushButton("Generate graph")
self.graphButton.show()
self.graphButton.clicked.connect(self.showGraph)
rows += 1
paramLayout.addWidget(self.graphButton, rows, 0)
self.lemsViewButton = QPushButton("Generate LEMS View")
self.lemsViewButton.show()
self.lemsViewButton.clicked.connect(self.showLemsView)
rows += 1
paramLayout.addWidget(self.lemsViewButton, rows, 0)
self.image3DButton = QPushButton("Generate 3D image")
self.image3DButton.show()
self.image3DButton.clicked.connect(self.show3Dimage)
rows += 1
paramLayout.addWidget(self.image3DButton, rows, 0)
self.matrixButton = QPushButton("Generate matrix")
self.matrixButton.show()
self.matrixButton.clicked.connect(self.showMatrix)
rows += 1
paramLayout.addWidget(self.matrixButton, rows, 0)
self.nml2Button = QPushButton("Generate NeuroML 2")
self.nml2Button.show()
self.nml2Button.clicked.connect(self.generateNeuroML2)
rows += 1
paramLayout.addWidget(self.nml2Button, rows, 0)
rows += 1
l = QLabel("Simulation parameters")
l.setFont(header_font)
paramLayout.addWidget(l, rows, 0)
self.sim_entries = {}
svars = ['dt', 'duration', 'seed']
for s in svars:
rows += 1
sval = self.simulation.__getattr__(s)
if sval is not None:
label = QLabel("%s" % s)
paramLayout.addWidget(label, rows, 0)
entry = self.get_value_entry(s, sval, self.sim_entries)
paramLayout.addWidget(entry, rows, 1)
rows += 1
paramLayout.addWidget(QLabel("Simulator:"), rows, 0)
self.simulatorComboBox = QComboBox(self)
for sim in self.simulators:
self.simulatorComboBox.addItem(sim)
paramLayout.addWidget(self.simulatorComboBox, rows, 1)
rows += 1
self.runButton = QPushButton("Run simulation")
self.runButton.show()
self.runButton.clicked.connect(self.runSimulation)
self.autoRunCheckBox = QCheckBox("Auto run")
rows += 1
paramLayout.addWidget(self.runButton, rows, 0)
paramLayout.addWidget(self.autoRunCheckBox, rows, 1)
mainLayout.addLayout(topLayout, 0, 1)
mainLayout.addLayout(paramLayout, 1, 0)
mainLayout.addLayout(midLayout, 1, 1)
#self.setLayout(paramLayout)
self.setLayout(mainLayout)
self.setWindowTitle("NeuroMLlite GUI")
self.update_network_json()
self.update_simulation_json()
